I had a similar-ish experience last year at SFO. Was on a TP run so was flying back home via SFO-JFK-LHR-MAD / MAN. At the lounge in SFO I noticed that an upgrade seat in the rare A bucket became available on my flight to JFK. I called the GGL line and the agent could see it but it was taking a long time to process. By this point boarding just started and I informed the gate agent that I was being reticketed from J to F on the flight. She asked for my details and said that I was no longer on the flight and that my seat in J had been given to someone else. The GGL agent still couldn’t reticket me so I ended up missing the flight and having to re-route via ORD back home which als meant spending the night in ORD due to storms. At least tv agent was able to secure my new itinerary.
I learned never to make changes to a ticket close to departure.